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- PDB-1iu6: Neutron Crystal Structure of the rubredoxin mutant from Pyrococcu... -

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Basic information

Entry
Database: PDB / ID: 1iu6
TitleNeutron Crystal Structure of the rubredoxin mutant from Pyrococcus Furiosus
Componentsrubredoxin
KeywordsELECTRON TRANSPORT / rubredoxin / mutant / hydrogen / hydration / thermostability
Function / homology
Function and homology information


alkane catabolic process / electron transfer activity / iron ion binding
Similarity search - Function
Rubredoxin / : / Rubredoxin, iron-binding site / Rubredoxin signature. / Rubrerythrin, domain 2 - #10 / Rubredoxin domain / Rubredoxin / Rubredoxin-like domain / Rubredoxin-like domain profile. / Rubrerythrin, domain 2 ...Rubredoxin / : / Rubredoxin, iron-binding site / Rubredoxin signature. / Rubrerythrin, domain 2 - #10 / Rubredoxin domain / Rubredoxin / Rubredoxin-like domain / Rubredoxin-like domain profile. / Rubrerythrin, domain 2 / Single Sheet / Mainly Beta
Similarity search - Domain/homology
DEUTERATED WATER / : / Rubredoxin
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodNEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsChatake, T. / Kurihara, K. / Tanaka, I. / Tsyba, I. / Bau, R. / Jenney, F.E. / Adams, M.W.W. / Niimura, N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: A neutron crystallographic analysis of a rubredoxin mutant at 1.6 A resolution.
Authors: Chatake, T. / Kurihara, K. / Tanaka, I. / Tsyba, I. / Bau, R. / Jenney, F.E. / Adams, M.W. / Niimura, N.
History
DepositionFeb 27, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Nov 28, 2018Group: Data collection / Category: diffrn_detector / diffrn_source
Item: _diffrn_detector.details / _diffrn_detector.detector ..._diffrn_detector.details / _diffrn_detector.detector / _diffrn_detector.type / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type
Revision 1.5Dec 5, 2018Group: Data collection / Category: diffrn_radiation / Item: _diffrn_radiation.pdbx_scattering_type
Revision 1.6Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.7Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: rubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,9192
Polymers5,8631
Non-polymers561
Water55831
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.480, 35.700, 43.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein rubredoxin


Mass: 5863.470 Da / Num. of mol.: 1 / Mutation: W3Y, I23V, L32I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: P24297
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

ExperimentMethod: NEUTRON DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growMethod: vapor diffusion / Details: Na/K phosphate, VAPOR DIFFUSION
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Details: used macroseeding, Bau, R., (1998) J.BIOL.INORG.CHEM., 3, 484.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
140 mg/mlprotein1drop
250 mMTris-HCl1drop
30.3 M1dropNaCl
43.6 Msodium potassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 299 K
Diffraction sourceSource: NUCLEAR REACTOR / Site: JRR-3M / Beamline: 1G-A / Wavelength: 2.345 Å
DetectorDetector: DIFFRACTOMETER / Date: Nov 15, 2000 / Details: JAERI BIX-3
RadiationMonochromator: ELASTICALLY-BENT PERFECT SILICON MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: neutron
Radiation wavelengthWavelength: 2.345 Å / Relative weight: 1
ReflectionResolution: 1.6→100 Å / Num. all: 6584 / Num. obs: 6584 / % possible obs: 87.5 % / Redundancy: 2.9 % / Biso Wilson estimate: 9.1 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 19.5
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.254 / % possible all: 66
Reflection
*PLUS
Lowest resolution: 100 Å / Num. measured all: 19385
Reflection shell
*PLUS
% possible obs: 66 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→10 Å / Isotropic thermal model: Istotropic / σ(F): 3
RfactorNum. reflectionSelection details
Rfree0.228 690 RANDOM
Rwork0.201 --
obs-6308 -
Displacement parametersBiso mean: 13.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms393 0 1 29 423
Refine LS restraints
Refine-IDTypeDev ideal
NEUTRON DIFFRACTIONc_bond_d0.007
NEUTRON DIFFRACTIONc_angle_deg1.6
LS refinement shellResolution: 1.6→1.7 Å /
Rfactor% reflection
Rfree0.329 -
Rwork0.285 -
obs-65 %
Refinement
*PLUS
Lowest resolution: 10 Å / Rfactor Rfree: 0.23 / Rfactor Rwork: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS

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